Machado, C. R. L. | Search bioRxiv

bioRxiv2025

Spatial transcriptomics reveals distinct inflammatory and adaptive immune properties of rheumatoid arthritis synovial fibroblasts

ObjectiveRheumatoid arthritis (RA) synovium displays cellular heterogeneity, with gene expression driving pathogenesis. Prior transcriptomic studies relied on disaggregated tissue, which causes cell loss and induction. We applied spatial transcriptomics to investigate synovial lining and sublining fibroblasts and macrophages from RA and osteoarthritis (OA) patients. MethodsFresh frozen synovial tissues from 7 RA and 8 OA patients were analyzed using the NanoString GeoMX DSP Whole Transcriptome Assay. Lining and sublining regions were segmented into fibroblasts and macrophages. Principal component analysis separated samples by cell type and disease. Differentially expressed genes (DEG) were analyzed by linear mixed models (p-value<0.05 and |log2 fold change|>0.5) and Reactome pathway (FDR<0.02) analysis. ResultsDEG analysis of RA compared to OA revealed distinct gene signatures across regions and cell types. RA lining fibroblasts exhibited a strong pro-inflammatory and matrix-destructive signature, while RA sublining fibroblasts showed an unexpected role in antigen presentation and adaptive immunity. RA lining macrophages exhibited enrichment for interleukin signaling, extracellular matrix organization, and translation-related pathways. In contrast, sublining macrophages showed minimal transcriptional differences between RA and OA, suggesting limited pathogenic involvement. Comparison between lining and sublining within RA showed that lining fibroblasts display a higher activated phenotype than sublining cells. ConclusionSpatial transcriptomic analysis uncovers distinct region- and cell-type-specific transcriptional profiles in RA synovium. Lining fibroblasts are highly activated and destructive, and sublining fibroblasts contribute surprisingly to adaptive immunity. This data provides clues to region-cell-type-specific functions that could be exploited to identify novel therapeutic targets.

immunology↗

bioRxiv2024

Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity

The mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific FLS biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors (TFs) and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF-stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an activated state relative to the resting state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.

bioinformatics↗